[Bioperl-l] New enzymes for RestrictionEnzyme.pm

Brian Osborne brian_osborne@cognia.com
Wed, 14 Aug 2002 12:39:26 -0400


Ryan,

Good. If you don't mind I'll put this into the scripts/contributed directory
under your name, which is for useful scripts which don't use Bioperl.

Brian O.

-----Original Message-----
From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
Behalf Of Ryan Brinkman
Sent: Wednesday, August 14, 2002 12:27 PM
To: bioperl-l@bioperl.org; sac@bioperl.org; brian_osborne@cognia.com
Subject: RE: [Bioperl-l] New enzymes for RestrictionEnzyme.pm


This seems to work.

Cheers,
Ryan

#!/usr/bin/perl
# Generate an updated rebase enzyme list

my $strider=@ARGV[0]; #commercial_version_rebase_strider_format

open (FILEIN,$strider) or die "can't open $strider:$!\n";

while (<FILEIN>){
  chomp;
 # print "a:$_\n";
  unless (/#/){
   # print "b\n";
    ($enzyme,$cutsite)=split(',');
  #  print "c:$cutsite\n";
    if ($cutsite =~ m#/#){
  #    print "match $-[0]\n";

      $match=$-[0];
    }
    ($seqfixed=$cutsite) =~ s/\///g;
    $seqfixed=uc $seqfixed;
    #print "s:$seqfixed\n";
    print " \'$enzyme\'\t=> \'".$seqfixed." ".$match."\'\,\n";
  }
}


>>> "Brian Osborne" <brian_osborne@cognia.com> 08/14/02 06:25AM >>>
Ryan and Steve,

Ryan, thank you for pointing this out, we'll update.

Steve C., you mention a converter script, rebase2perl.pl, in
RestrictionEnzyme.pm. Do you know where this is and/or can you send it to
me?

Thanks again,

Brian O.

-----Original Message-----
From: bioperl-l-admin@bioperl.org [mailto:bioperl-l-admin@bioperl.org]On
Behalf Of Ryan Brinkman
Sent: Monday, August 12, 2002 8:13 PM
To: bioperl-l@bioperl.org
Cc: sac@bioperl.org
Subject: [Bioperl-l] New enzymes for RestrictionEnzyme.pm


I just had occasion to use  RestrictionEnzyme.pm, and noticed the list may
be out of date (a comment says it was built on a version dated Jan 29 98").
I think the following entries can be added based on my parsing of the latest
version of rebase (Aug 01 2002)

'Acc65I'        => 'GGTACC 1',
 'AceII'        => 'GCTAGC 5',
 'Asp718I'      => 'GGTACC 1',
 'BbeI'         => 'GGCGCC 5',
 'BfrBI'        => 'ATGCAT 3',
 'Bme1580I'     => 'GKGCMC 5',
 'BseBI'        => 'CCWGG 2',
 'BseSI'        => 'GKGCMC 5',
 'BsiLI'        => 'CCWGG 2',
 'Bsp120I'      => 'GGGCCC 1',
 'BssKI'        => 'CCNGG 0',
 'BssNAI'       => 'GTATAC 3',
 'Bst1107I'     => 'GTATAC 3',
 'BstAPI'       => 'GCANNNNNTGC 7',
 'BstKTI'       => 'GATC 3',
 'BstNI'        => 'CCWGG 2',
 'BstOI'        => 'CCWGG 2',
 'BstSCI'       => 'CCNGG 0',
 'Bst2UI'       => 'CCWGG 2',
 'BstZ17I'      => 'GTATAC 3',
 'BthCI'        => 'GCNGC 4',
 'Cfr9I'        => 'CCCGGG 1',
 'ChaI'         => 'GATC 4',
 'Csp6I'        => 'GTAC 1',
 'CviAII'       => 'CATG 1',
 'Ecl136II'     => 'GAGCTC 3',
 'EcoHI'        => 'CCSGG 0',
 'EcoICRI'      => 'GAGCTC 3',
 'EcoT22I'      => 'ATGCAT 5',
 'EgeI'         => 'GGCGCC 3',
 'EheI'         => 'GGCGCC 3',
 'EsaBC3I'      => 'TCGA 2',
 'FatI'         => 'CATG 0',
 'FmuI'         => 'GGNCC 4',
 'FspAI'        => 'RTGCGCAY 4',
 'Hin6I'        => 'GCGC 1',
 'HinP1I'       => 'GCGC 1',
 'Hpy8I'        => 'GTNNAC 3',
 'Hpy99I'       => 'CGWCG 5',
 'Hpy178III'    => 'TCNNGA 2',
 'Hpy188I'      => 'TCNGA 3',
 'Hpy188III'    => 'TCNNGA 2',
 'HpyCH4I'      => 'CATG 3',
 'HspAI'        => 'GCGC 1',
 'KasI'         => 'GGCGCC 1',
 'LpnI'         => 'RGCGCY 3',
 'Mph1103I'     => 'ATGCAT 5',
 'MroNI'        => 'GCCGGC 1',
 'MvaI'         => 'CCWGG 2',
 'NgoAIV'       => 'GCCGGC 1',
 'NgoMIV'       => 'GCCGGC 1',
 'Nli3877I'     => 'CYCGRG 5',
 'NsiI'         => 'ATGCAT 5',
 'OliI'         => 'CACNNNNGTG 5',
 'Ppu10I'       => 'ATGCAT 1',
 'PsiI'         => 'TTATAA 3',
 'Psp03I'       => 'GGWCC 4',
 'PspAI'        => 'CCCGGG 1',
 'PspOMI'       => 'GGGCCC 1',
 'PssI'         => 'RGGNCCY 5',
 'SciI'         => 'CTCGAG 3',
 'SelI'         => 'CGCG 0',
 'SfoI'         => 'GGCGCC 3',
 'Sse232I'      => 'CGCCGGCG 2',
 'TaiI'         => 'ACGT 4',
 'TauI'         => 'GCSGC 4',
 'TscI'         => 'ACGT 4',
 'UnbI'         => 'GGNCC 0',
 'VpaK11AI'     => 'GGWCC 0',
 'XmaI'         => 'CCCGGG 1',
 'XmaCI'        => 'CCCGGG 1',
 'ZraI'         => 'GACGTC 3',
 'Zsp2I'        => 'ATGCAT 5',



Thanks for a great module,
Ryan Brinkman
Xenon Genetics Inc.



*************************************************************************
This email message is confidential and may contain privileged information.
Any unauthorized dissemination or copying is strictly prohibited. If you
have received this message in error, please delete it and notify us
immediately.
< XGI >
_______________________________________________
Bioperl-l mailing list
Bioperl-l@bioperl.org
http://bioperl.org/mailman/listinfo/bioperl-l


_______________________________________________
Bioperl-l mailing list
Bioperl-l@bioperl.org
http://bioperl.org/mailman/listinfo/bioperl-l